Relative positional embeddings with RoPE
In language models, the order of tokens is of critical importance. This post explains RoPE: a technique that ensures that the pairwise token attention weights only depend on their relative position.
Fast and exact gap-affine partial order alignment with POASTA
Partial order alignment is a common method to compute multiple sequence alignments through iterative sequence-to-graph alignment. In this paper, we introduce a new algorithm that accelerates alignment by exploiting graph topology and shared sequence between the query and the graph.
Gut microbiome dysbiosis linked with recurrent UTIs
More than half of the women in the US get a urinary tract infection (UTI) in their lifetime, which frequently becomes recurrent. In this paper, we investigated the role of the gut microbiome in facilitating recurrence.
StrainGE: Strain Genome Explorer
StrainGE is a toolkit for tracking and characterizing low-abundance strains in complex microbial communities. It enables detailed insights into the bacterial strain-level diversity of whole metagenomic sequencing samples.
Using locality sensitive hashing to compactly represent k-mers
K-mers are frequently used in bioinformatics to profile and compare genomes. This article describes a technique for compactly representing long k-mers with locality-sensitive hashing.
Controlling a servo with an AVR microcontroller
Servos are useful small motors with applications in robotics, RC cars, and others. Here, we describe how to use an ATTiny44 to control its position.
